In a new study, researchers found that next-generation sequencing approaches to karyotyping provided more precision than conventional cytogenetic analysis (CCA) in identifying copy number alterations (CNAs) and other aberrations in acute myeloid leukemia (AML). The study results were published in the journal Blood Advances.
“Given the capability of sequencing techniques to assess CNAs and gene fusions, it is surprising that CCA still holds an unchallenged position in the routine diagnosis of AML,” the study investigators explained in their report.
A total of 281 patients with AML were evaluated in this study in Sweden. CCA, whole-transcriptome RNA sequencing (WTS), and shallow whole-genome sequencing (WGS) were compared using samples from each patient for karyotyping and prognostication of survival outcomes.
CCA and shallow WGS showed high concordance (average 96%) for identifying copy number alterations including del(5q), del(17p), and monosomy 7. While each technique identified aberrations that were not found using the other technique, shallow WGS showed higher accuracy.
The researchers also found that for assessing genomic complexity and identifying poor prognosis, a total genomic loss of 200 megabases or more identified by shallow WGS outperformed the use of CCA-based complex karyotype.
WTS showed high concordance (99%) with CCA for identifying gene fusions, and both approaches identified some fusions missed by the other. Sensitivity appeared to be superior with WTS, compared with CCA, but the sensitivity of WTS showed some dependency on sequencing depth.
This was exposed in a limitation in identifying PML-RARA fusions using WTS. WTS did, however, reveal multiple KMT2A rearrangements and 2 chromosome 16 inversions that were missed by CCA.
CCA and next-generation karyotyping approaches assessed in this study were used to classify patients into European LeukemiaNet categories. A total of 17 of the 281 patients were shifted into different risk categories when CCA was substituted with next-generation karyotyping in this analysis, reflecting a level of concordance of 94%. Prognostication of survival outcomes showed similar performance using either approach.
“The future will likely see advanced sequencing approaches, such as WGS at greater depth in combination with WTS applied in the clinical routine, displaying the full spectrum of molecular aberrations in AML,” the study authors reported.
The researchers noted that next-generation approaches currently have limitations regarding costs, validation, and capacity to quickly provide reliable results. However, they considered the approach used in this study to be comparable to CCA based on cost and time considerations.
Mareschal S, Palau A, Lindberg J, et al. Challenging conventional karyotyping by next-generation karyotyping in 281 intensively treated patients with AML. Blood Adv. 2021;5(4):1003-1016. doi:10.1182/bloodadvances.2020002517